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Proxl XML Converter Development Guide

This guide provides information for how to develop software to convert the output of a cross-linking proteomics pipeline to proxl XML suitable for import into proxl.

Proxl XML schema

Proxl XML files must adhere to the proxl XML schema, which may be found at https://github.com/yeastrc/proxl-import-api/tree/master/xsd. In addition to the assigned scores, descriptions of those scores (names, descriptions, and how to treat them) are incorporated into the schema, which allows proxl XML to describe data generated by nearly any pipeline.

HTML documentation for the schema can be found at http://yeastrc.org/proxl-xml-documentation/1.4/proxl-xml-v1.4.html. The root element is proxl_input. You may click on any attribute or element in the diagrams to navigate the schema.

An image containing the entire schema structure and documentation can be found at https://raw.githubusercontent.com/yeastrc/proxl-import-api/master/xsd/docs/proxl-input.png.

Example proxl XML file

Below is a very shortened, but valid, proxl XML file to illustrate the structure of the proxl XML schema. In this example StavroX was the analysis program and two peptides were identified, one of of which includes a cross-link.

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<proxl_input fasta_filename="gTuSC-parsimonious-plusRev.fasta">
    <search_program_info>
        <search_programs>
            <search_program name="StavroX" display_name="StavroX" version="3">
                <psm_annotation_types>
                    <filterable_psm_annotation_types>
                        <filterable_psm_annotation_type name="score" description="StavroX Score" filter_direction="above" default_filter="false" default_filter_value="50"/>
                        <filterable_psm_annotation_type name="FDR" description="False discovery rate" filter_direction="below" default_filter="true" default_filter_value="0.01"/>
                        <filterable_psm_annotation_type name="rank" description="Rank of PSM for scan" filter_direction="below" default_filter="true" default_filter_value="1"/>
                    </filterable_psm_annotation_types>
                    <descriptive_psm_annotation_types>
                        <descriptive_psm_annotation_type name="m/z" description="m/z"/>
                        <descriptive_psm_annotation_type name="obs. mass" description="obs. mass"/>
                        <descriptive_psm_annotation_type name="cand. mass" description="cand. mass"/>
                        <descriptive_psm_annotation_type name="deviation" description="deviation"/>
                        <descriptive_psm_annotation_type name="scan num." description="scan num."/>
                    </descriptive_psm_annotation_types>
                </psm_annotation_types>
            </search_program>
        </search_programs>
        <default_visible_annotations>
            <visible_psm_annotations>
                <search_annotation search_program="StavroX" annotation_name="scan num."/>
                <search_annotation search_program="StavroX" annotation_name="rank"/>
                <search_annotation search_program="StavroX" annotation_name="score"/>
                <search_annotation search_program="StavroX" annotation_name="FDR"/>
                <search_annotation search_program="StavroX" annotation_name="m/z"/>
                <search_annotation search_program="StavroX" annotation_name="obs. mass"/>
                <search_annotation search_program="StavroX" annotation_name="cand. mass"/>
                <search_annotation search_program="StavroX" annotation_name="deviation"/>
            </visible_psm_annotations>
        </default_visible_annotations>
    </search_program_info>
    <linkers>
        <linker name="dss">
            <crosslink_masses>
                <crosslink_mass mass="138.0681"/>
            </crosslink_masses>
        </linker>
    </linkers>
    <reported_peptides>
        <reported_peptide reported_peptide_string="[SFSLEKISAPDQR](K6)" type="unlinked">
            <peptides>
                <peptide sequence="SFSLEKISAPDQR">
                    <modifications>
                        <modification mass="138.0681" position="6" isMonolink="true"/>
                    </modifications>
                </peptide>
            </peptides>
            <psms>
                <psm scan_file_name="Q_2013_1010_RJ_07.mzML" scan_number="25982" precursor_charge="3">
                    <filterable_psm_annotations>
                        <filterable_psm_annotation search_program="StavroX" annotation_name="score" value="23"/>
                        <filterable_psm_annotation search_program="StavroX" annotation_name="rank" value="1"/>
                        <filterable_psm_annotation search_program="StavroX" annotation_name="FDR" value="0.0200"/>
                    </filterable_psm_annotations>
                    <descriptive_psm_annotations>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="m/z" value="545.2862"/>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="obs. mass" value="1633.8440"/>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="cand. mass" value="1633.8432"/>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="deviation" value="0.4885"/>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="scan num." value="25982"/>
                    </descriptive_psm_annotations>
                </psm>
            </psms>
        </reported_peptide>
        <reported_peptide reported_peptide_string="[KDVLLR](K1)--[TNQSSQEDFNNFMDSMKNESSLHLR](K17)" type="crosslink">
            <peptides>
                <peptide sequence="KDVLLR">
                    <linked_positions>
                        <linked_position position="1"/>
                    </linked_positions>
                </peptide>
                <peptide sequence="TNQSSQEDFNNFMDSMKNESSLHLR">
                    <linked_positions>
                        <linked_position position="17"/>
                    </linked_positions>
                </peptide>
            </peptides>
            <psms>
                <psm scan_file_name="Q_2013_1010_RJ_07.mzML" scan_number="29178" precursor_charge="5" linker_mass="138.0681">
                    <filterable_psm_annotations>
                        <filterable_psm_annotation search_program="StavroX" annotation_name="score" value="28"/>
                        <filterable_psm_annotation search_program="StavroX" annotation_name="rank" value="1"/>
                        <filterable_psm_annotation search_program="StavroX" annotation_name="FDR" value="0.0000"/>
                    </filterable_psm_annotations>
                    <descriptive_psm_annotations>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="m/z" value="768.7731"/>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="obs. mass" value="3839.8366"/>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="cand. mass" value="3839.8327"/>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="deviation" value="1.0017"/>
                        <descriptive_psm_annotation search_program="StavroX" annotation_name="scan num." value="29178"/>
                    </descriptive_psm_annotations>
                </psm>
            </psms>
        </reported_peptide>
    </reported_peptides>
    <matched_proteins>
        <protein sequence="MEIKEVDDRAELLRYTNNIPLLGKLVNHQPLWSTNPKLKSFSLEKISAPDQRRVQEALVVKDLLNVLIGLEGTYIRYFNDYEPSDPETPIEFKIAKKMDPSFKTFSRRIVRYGKQYMILTRAYEKWSDTSFGMVLQRFAYEIRRFLEDVYLKTLVERLERDFNKVPNFSIRELEQIINETEVNKQMELLYNIYEEIFREIEERRTNQSSQEDFNNFMDSMKNESSLHLRLMVAFDTTVYPVPKGGAILKIFQQKILENLGDRSSVMFLKKLLNNISQDYCTMLYEWLTQGILNDPYQEFMTYDDLEGKTDNIFDTRDRAWDTQYFIRKDVLLRDCDSEEDKNLLFKMLRTGILLKVVRASLQIPTIPSNSSDITIQEINDFADLMEGSNLELYVDKCYSRANEIFLKLFFQGYDLINVLKHLQQIFLGYQSGHNVLKFLTKNMGELTKHYRNDNNANYDKLLQNFELERQSENPNNLMRQLLMIQFDTETLPQVLSHYLQIYPEVPENNSANDDSDPLMHANNFKNMNAILFDELSKERTGAYHGSNLELYTPKSAIYHLKFDINIPYPLNIIISRTCMIKYQIILRYQLVLQYHSRLLDETWMDLNKTPSWKYRGYSHTVKRRIVRATRVLHAKMNHFIKTIMEYFNQNVIDKEVYSLEKCYRNPTLAVAIQNELEGGLTNIMTNRCLSDLIPLQLQIFDIVYKFCKFIKSMRAKLCQLDPVLYEKHKSGMMKTLNEGYRTNNGGQEDVGYQEDAALELIQKLIEYISNASSIFRKCLINFTQELSTEKFDFYDSSSVDAAGIERVLYSIVPPRSASASSQR">
            <protein_annotation name="Spc97-yeast"/>
        </protein>
        <protein sequence="MELEPTLFGIIEALAPQLLSQSHLQTFVSDVVNLLRSSTKSATQLGPLIDFYKLQSLDSPETTIMWHKIEKFLDALFGIQNTDDMVKYLSVFQSLLPSNYRAKIVQKSSGLNMENLANHEHLLSPVRAPSIYTEASFENMDRFSERRSMVSSPNRYVPSSTYSSVTLRQLSNPYYVNTIPEEDILKYVSYTLLATTSALFPFDHEQIQIPSKIPNFESGLLHLIFEAGLLYQSLGYKVEKFRMLNISPMKKALIIEISEELQNYTAFVNNLVSSGTVVSLKSLYREIYENIIRLRIYCRFTEHLEELSGDTFLIELNIFKSHGDLTIRKIATNLFNSMISLYYEYLMNWLTKGLLRATYGEFFIAENTDTNGTDDDFIYHIPIEFNQERVPAFIPKELAYKIFMIGKSYIFLEKYCKEVQWTNEFSKKYHVLYQSNSYRGISTNFFEIINDQYSEIVNHTNQILNQKFHYRDVVFALKNILLMGKSDFMDALIEKANDILATPSDSLPNYKLTRVLQEAVQLSSLRHLMNSPRNSSVINGLDARVLDLGHGSVGWDVFTLDYILYPPLSLVLNVNRPFGRKEYLRIFNFLWRFKKNNYFYQKEMLKSNDIIRSFKKIRGYNPLIRDIINKLSRISILRTQFQQFNSKMESYYLNCIIEENFKEMTRKLQRTENKSQNQFDLIRLNNGTIELNGILTPKAEVLTKSSSSKPQKHAIEKTLNIDELESVHNTFLTNILSHKLFATNTSEISVGDYSGQPYPTSLVLLLNSVYEFVKVYCNLNDIGYEIFIKMNLNDHEASNGLLGKFNTNLKEIVSQYKNFKDRLYIFRADLKNDGDEELFLLSKSLR">
            <protein_annotation name="Spc98-yeast"/>
        </protein>
        <protein sequence="MHHHHHHGKPIPNPLLGLDSTENLYFQGIDPFTMGGEIITLQAGQCGNHVGKFLWSQLAKEHAIGTDGLSQLPDSSTERDDDTKPFFRENSRNKFTPRAIMMDSEPSVIADVENTFRGFFDPRNTWVASDGASAGNSWANGYDIGTRNQDDILNKIDKEIDSTDNFEGFQLLHSVAGGTGSGLGSNLLEALCDRYPKKILTTYSVFPARSSEVVVQSYNTILALRRLIEDSDATVVFDNASLLNISGKVFRNPNIDLQHTNQLISTIISSVTNSIRFPSYMYSSMSSIYSTLIPSPELHFLSPSFTPFTSDYIHDDIAHKGHSSYDVMLDLLDPSNSLVSTAMNNPTYFNVYNTIIGNVEPRQISRAMTKLQQRIKFPSWSSSAMHVNIGRRSPYLPLQPNENEVSGMMLSNMSTVVNVFENACNTFDKVFAKGAFLNNYNVGDLFQSMQNVQDEFAESREVVQSLMEDYVAAEQDSYLDDVLVDDENMVGELEEDLDADGDHKLV">
            <protein_annotation name="His-TEV-Tub4-yeast"/>
        </protein>
    </matched_proteins>
    <static_modifications>
        <static_modification amino_acid="C" mass_change="57.0215"/>
    </static_modifications>
    <decoy_labels>
        <decoy_label prefix="random_seq"/>
    </decoy_labels>
</proxl_input>

Writing the conversion software

Your software will read in the native output of your respective cross-linking search software and re-represent it as proxl XML. The converter software may be written in any programming or scripting language, so long as valid proxl XML is produced.

We have developed several open-source converters in Java, which may be used as examples. Follow the links below to access the source code associated with each converter:

For any assistance developing converters, please email us at proxl-help@yeastrc.org.